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- PDB-8clk: TFIIIC TauA complex -

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Basic information

Entry
Database: PDB / ID: 8clk
TitleTFIIIC TauA complex
Components
  • General transcription factor 3C polypeptide 1
  • General transcription factor 3C polypeptide 3
  • General transcription factor 3C polypeptide 5
  • General transcription factor 3C polypeptide 6
KeywordsTRANSCRIPTION / TFIIIC / tRNA gene / B-Box promoter / DNA recognition
Function / homology
Function and homology information


tRNA transcription / 5S class rRNA transcription by RNA polymerase III / transcription factor TFIIIC complex / RNA polymerase III general transcription initiation factor activity / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Abortive And Retractive Initiation / transcription initiation at RNA polymerase III promoter / skeletal muscle cell differentiation / tRNA transcription by RNA polymerase III ...tRNA transcription / 5S class rRNA transcription by RNA polymerase III / transcription factor TFIIIC complex / RNA polymerase III general transcription initiation factor activity / RNA Polymerase III Transcription Initiation From Type 1 Promoter / RNA Polymerase III Transcription Initiation From Type 2 Promoter / RNA Polymerase III Abortive And Retractive Initiation / transcription initiation at RNA polymerase III promoter / skeletal muscle cell differentiation / tRNA transcription by RNA polymerase III / rRNA transcription / transcription by RNA polymerase III / fibrillar center / nuclear membrane / nuclear body / ribonucleoprotein complex / nucleolus / DNA binding / nucleoplasm / membrane
Similarity search - Function
TFIIIC subunit GTF3C6-like / Transcription factor IIIC subunit 5, HTH domain / Transcription factor TFIIIC, triple barrel domain / Transcription factor Tfc4/TFIIIC-102/Sfc4 / Transcription factor IIIC subunit Tfc1/Sfc1 / Transcription factor IIIC subunit Tfc1/Sfc1, triple barrel domain / TFIIIC, subcomplex tauA subunit Sfc1, triple barrel domain superfamily / RNA polymerase III transcription factor (TF)IIIC subunit HTH domain / TFIIIC subunit triple barrel domain / Tau95 Triple barrel domain ...TFIIIC subunit GTF3C6-like / Transcription factor IIIC subunit 5, HTH domain / Transcription factor TFIIIC, triple barrel domain / Transcription factor Tfc4/TFIIIC-102/Sfc4 / Transcription factor IIIC subunit Tfc1/Sfc1 / Transcription factor IIIC subunit Tfc1/Sfc1, triple barrel domain / TFIIIC, subcomplex tauA subunit Sfc1, triple barrel domain superfamily / RNA polymerase III transcription factor (TF)IIIC subunit HTH domain / TFIIIC subunit triple barrel domain / Tau95 Triple barrel domain / B-block binding subunit of TFIIIC / Tfc3, extended winged-helix domain / Transcription facto Tfc3-like / B-block binding subunit of TFIIIC / Tetratricopeptide repeat / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
General transcription factor 3C polypeptide 1 / General transcription factor 3C polypeptide 6 / General transcription factor 3C polypeptide 5 / General transcription factor 3C polypeptide 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSeifert-Davila, W. / Girbig, M. / Hauptmann, L. / Hoffmann, T. / Eustermann, S. / Mueller, C.W.
Funding support Germany, 1items
OrganizationGrant numberCountry
Other government Germany
CitationJournal: Sci Adv / Year: 2023
Title: Structural insights into human TFIIIC promoter recognition.
Authors: Wolfram Seifert-Davila / Mathias Girbig / Luis Hauptmann / Thomas Hoffmann / Sebastian Eustermann / Christoph W Müller /
Abstract: Transcription factor (TF) IIIC recruits RNA polymerase (Pol) III to most of its target genes. Recognition of intragenic A- and B-box motifs in transfer RNA (tRNA) genes by TFIIIC modules τA and τB ...Transcription factor (TF) IIIC recruits RNA polymerase (Pol) III to most of its target genes. Recognition of intragenic A- and B-box motifs in transfer RNA (tRNA) genes by TFIIIC modules τA and τB is the first critical step for tRNA synthesis but is mechanistically poorly understood. Here, we report cryo-electron microscopy structures of the six-subunit human TFIIIC complex unbound and bound to a tRNA gene. The τB module recognizes the B-box via DNA shape and sequence readout through the assembly of multiple winged-helix domains. TFIIIC220 forms an integral part of both τA and τB connecting the two subcomplexes via a ~550-amino acid residue flexible linker. Our data provide a structural mechanism by which high-affinity B-box recognition anchors TFIIIC to promoter DNA and permits scanning for low-affinity A-boxes and TFIIIB for Pol III activation.
History
DepositionFeb 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 21, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Jul 19, 2023Group: Data collection / Database references / Category: citation / citation_author / pdbx_validate_planes
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _pdbx_validate_planes.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: General transcription factor 3C polypeptide 1
D: General transcription factor 3C polypeptide 3
E: General transcription factor 3C polypeptide 5
F: General transcription factor 3C polypeptide 6


Theoretical massNumber of molelcules
Total (without water)431,1274
Polymers431,1274
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, Mass photometry was performed to assess complex integrity
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein General transcription factor 3C polypeptide 1 / TF3C-alpha / TFIIIC box B-binding subunit / Transcription factor IIIC 220 kDa subunit / TFIIIC 220 ...TF3C-alpha / TFIIIC box B-binding subunit / Transcription factor IIIC 220 kDa subunit / TFIIIC 220 kDa subunit / TFIIIC220 / Transcription factor IIIC subunit alpha


Mass: 244200.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF3C1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q12789
#2: Protein General transcription factor 3C polypeptide 3 / Transcription factor IIIC 102 kDa subunit / TFIIIC 102 kDa subunit / TFIIIC102 / Transcription ...Transcription factor IIIC 102 kDa subunit / TFIIIC 102 kDa subunit / TFIIIC102 / Transcription factor IIIC subunit gamma / TF3C-gamma


Mass: 101387.969 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF3C3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y5Q9
#3: Protein General transcription factor 3C polypeptide 5 / TF3C-epsilon / Transcription factor IIIC 63 kDa subunit / TFIIIC 63 kDa subunit / TFIIIC63 / ...TF3C-epsilon / Transcription factor IIIC 63 kDa subunit / TFIIIC 63 kDa subunit / TFIIIC63 / Transcription factor IIIC subunit epsilon


Mass: 61468.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF3C5, CDABP0017 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y5Q8
#4: Protein General transcription factor 3C polypeptide 6 / Transcription factor IIIC 35 kDa subunit / TFIIIC 35 kDa subunit / TFIIIC35 / Transcription factor ...Transcription factor IIIC 35 kDa subunit / TFIIIC 35 kDa subunit / TFIIIC35 / Transcription factor IIIC subunit 6


Mass: 24069.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GTF3C6, C6orf51, CDA020, NPD020 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q969F1

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: TFIIIC TauA subcomplex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.33 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: UltrAuFoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 6 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1700 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 42.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55079 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 117.64 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.005211021
ELECTRON MICROSCOPYf_angle_d0.75214904
ELECTRON MICROSCOPYf_chiral_restr0.04661670
ELECTRON MICROSCOPYf_plane_restr0.00891910
ELECTRON MICROSCOPYf_dihedral_angle_d13.30314134

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